I have a 1999 Honda Civic CNG with 140,000 highway miles. Initially, while driving the car at highway speed, the check engine light would flash and the car would lose power. I would have to stop and turn the car off for a minute and then resume driving. The codes stated "misfire". I replaced the catalytic converter and fuel filter. This solved the problem for a few months, but now it has resumed with the same symptoms and is now happening more at lower speeds. It doesn't matter what the operating temp is. This is always indicated by the check engine light coming on just prior to it flashing.
It sounds as if any questions have already been answered:
The codes stated "misfire". Replace Cat and fuel filter.
The flash and loss of power is almost certainly a limp home mode: the engine computer has detected a problem that it considers serious enough that it needs fixing as soon as possible. However, the manufacturer doesn't want to leave you stranded so the vehicle will continue to limp along. By turning the car off, you're briefly defeating the limp mode but the root problem hasn't been addressed.
The increase in frequency indicates that the problem is getting worse.
Could be lots of things. Fuel pressure regulator, spark plugs, catalytic converter, O2 sensor(s), fuel injectors, fuel filter, even spark plug wires. I'd start by replacing the cheapest things first (distributor, plugs, wires and fuel filter) and see if that helps. Also pull the catalytic converter and see if there's any obvious damage inside. Anything else you'll probably have to take it to a mechanic who knows about these cars.